InSNP is a program that detects substitution and indel SNPs in sequencing traces. It uses simple algorithms to detect the mutations and presents the sequences in compact visualizations that let you quickly decide which ones are real.
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Manaster C, Zheng W, Teuber M, W?chter S, D?ring F, Schreiber S, Hampe J (2005).
InSNP: A tool for automated detection and visualization of SNPs and InDels.
Human Mutation 26(1): 11-19